Simultaneous estimation of genetic linkage and preferential pairing factor for a triploid population with unphased markers

Jian Xin Wang, Xiao Li Dong, Xiao Ming Pang, Ya Fei Lü, Hua Lin Yi, Xiao Xia Yang, Zhong Wang, Song Wu, Rong Ling Wu

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

Abstract

Triploids, recognized to occur more frequently in natural and experimental populations of many species than previously appreciated, display important economic and biological values. Despite this, however, linkage analysis for triploids has not been well explored. We develop a statistical model for estimating and testing the linkage between molecular markers in a triploid population derived from a tetraploid and diploid parent. The model incorporates one important meiotic feature of tetraploids by which more homologous chromosomes pair with a greater likelihood than less homologous chromosomes. By implementing the EM algorithm within the maximum likelihood framework, the model provides a procedure for simultaneous estimation of the linkage and preferential pairing factor. The model accommodates the segregating patterns of pseudotest markers and intercross markers with different amounts of informativeness. The utility of the model was validated through a real data analysis and simulation studies. The model provides a statistical tool for linkage analysis in a triploid population by taking into account meiotic behavior of tetraploids. Results from the model will help to shed light on the genetic diversity and origin of a polyploid population.

Original languageEnglish (US)
Pages (from-to)2711-2720
Number of pages10
JournalChinese Science Bulletin
Volume57
Issue number21
DOIs
StatePublished - Jul 2012

All Science Journal Classification (ASJC) codes

  • General

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